Investigations on the pattern of linkage disequilibrium and selection signatures in the genomes of German Piétrain pigs

Abstract

The aim of this study was to study the population structure, to characterize the LD structure and to define core regions based on low recombination rates among SNP pairs in the genome of Piétrain pigs using data from the PorcineSNP60 BeadChip. This breed is a European sire line and was strongly selected for lean meat content during the last decades. The data were used to map signatures of selection using the REHH test. In the first step, selection signatures were searched genome-wide using only core haplotypes having a frequency above 0.25. In the second step, the results from the selection signature analysis were matched with the results from the recently conducted genome-wide association study for economical relevant traits to investigate putative overlaps of chromosomal regions. A small subdivision of the population with regard to the geographical origin of the individuals was observed. The extent of LD was determined genome-wide using r(2) values for SNP pairs with a distance ≤5 Mb and was on average 0.34. This comparable low r(2) value indicates a high genetic diversity in the Piétrain population. Six REHH values having a p-value < 0.001 were genome-wide detected. These were located on SSC1, 2, 6 and 17. Three positional candidate genes with potential biological roles were suggested, called LOC100626459, LOC100626014 and MIR1. The results imply that for genome-wide analysis especially in this population, a higher marker density and higher sample sizes are required. For a number of nine SNPs, which were successfully annotated to core regions, the REHH test was applied. However, no selection signatures were found for those regions (p-value < 0.1).

Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip

“…4). As expected, most tightly linked SNP pairs have the highest r 2 and average r 2 rapidly decreases as distance increases, with a similar pattern to what has been observed in previous studies in pigs and in other species 42–45 . Values of r 2 at short distances (0.00–0.05 Mb) ranged from 0.305 (Nero Siciliano) to 0.595 (Mora Romagnola); and at long distances (45–50 Mb) r 2 values ranged from 0.028 (Iberian) to 0.089 (Casertana).…”

Host Genome Influence on Gut Microbial Composition and Microbial Prediction of Complex Traits in Pigs

“…The pigs belonged to the Piétrain breed. This is an important sire line breed (Stratz et al 2014) for which genomic selection is practiced (Wellmann et al 2013). Housing, slaughtering, and the recording of phenotypes of the pigs was performed under standardized conditions at one experimental farm.…”

Invited review: Genome-wide association analysis for quantitative traits in livestock – a selective review of statistical models and experimental designs

“…The following example illustrates this. Stratz et al (2014) investigated the LD structure of a segregating Piétrain pig population. They used SNP chip genotypes (porcine 60K BeadChip, Illumina Inc., San Diego, CA) of nearly 900 Piétrain boars for the LD r 2 calculation for SNP pairs with a maximum distance of 5 megabases (Mb).…”